Publications co-authored by the Bioinformatics Core Facility

2019

Aparisi Rey A, Karaulanov E, Sharopov S, Arab K, Schäfer A, Gierl M, Guggenhuber S, Brandes C, Pennella L, Gruhn WH, Jelinek R, Maul C, Conrad A, Kilb W, Luhmann HJ, Niehrs C and Lutz B. (2019). Gadd45α modulates aversive learning through post‐transcriptional regulation of memory‐related mRNAs. EMBO Rep, doi: 10.15252/embr.201846022. Link

Arab K, Karaulanov E, Musheev M, Trnka P, Schäfer A, Grummt I# and Niehrs C#. (2019). GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet, 51: 217–223. (#indicates joint correspondence) Link

Akhtar J, Kreim N, Marini F, Mohana G, Brüne D, Binder H and Roignant JY. (2019). Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun, 10: 521. Link

2018

Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF. (2018). GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J, 37: e99325. Link

Becker K, Bluhm A*, Casas-Vila N*, Dinges N*, Dejung M, Sayols S, Kreutz C, Roignant JY, Butter F# and Legewie S#. (2018). Quantifying post-transcriptional regulation in the development of Drosophila melanogaster. Nat Commun, 9: 4970. (*indicates joint contribution, #indicates joint correspondence) Link

Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA and Beli P. (2018). p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Nat Commun, 9: 1017. Link

Braun S*, Enculescu M*, Setty ST*, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S#, König J# and Zarnack K#. (2018). Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun, 9: 3315.(*indicates joint contribution, #indicates joint correspondence) Link

Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA and Beli P. (2018). Proteomic profiling of VCP substrates links VCP to K6‐linked ubiquitylation and c‐Myc function. EMBO Rep, 19: e44754. Link

Kaymak A, Sayols S, Papadopoulu T and Richly H. (2018). Role for the transcriptional activator ZRF1 in early metastatic events in breast cancer progression and endocrine resistance. Oncotarget, 9: 28666–28690. Link

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M and Roignant JY. (2018). Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes Dev, 32: 415–429. Link

Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR and Backofen R. (2018). Freiburg RNA tools: A central online resource for RNA-focused research and teaching. Nucleic Acids Res, 46: W25-W29.  Link

Sanchez-Mut JV, Heyn H, Silva BA, Dixsaut L, Garcia-Esparcia P, Vidal E, Sayols S, Glauser L, Monteagudo-Sánchez A, Perez-Tur J, Ferrer I, Monk D, Schneider B, Esteller M and Gräff J. (2018). PM20D1 is a quantitative trait locus associated with Alzheimer's disease. Nat Med, 24: 598–603. Link

Schäfer A, Mekker B, Mallick M, Vastolo V, Karaulanov E, Sebastian D, von der Lippen C, Epe B, Downes DJ, Scholz C and Niehrs C. (2018). Impaired DNA demethylation of C/EBP sites causes premature aging. Genes Dev, 32: 742–762. Link

Sutandy FXR*, Ebersberger S*, Huang L*, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S# and König# J. (2018). In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Res, 28: 699–713. (*indicates joint contribution, #indicates joint correspondence) Link

Tristán-Flores FE, Guzmán P, Ortega-Kermedy MS, Cruz-Torres G, de la Rocha C, Silva-Martínez GA, Rodríguez-Ríos D, Alvarado-Caudillo Y, Barbosa-Sabanero G, Sayols S, Lund G and Zaina S. (2018). Liver X receptor-binding DNA motif associated with atherosclerosis-specific DNA methylation profiles of Alu elements and neighboring CpG islands. J Am Heart Assoc, 7: e007686.  Link

Uhrig S and Klein H. (2018) PingPongPro: A tool for the detection of piRNA-mediated transposon silencing in small RNA-Seq data. Bioinformatics: 2: 335–336. Link

2017

Borriello F, Iannone R, Di Somma S, Vastolo V, Petrosino G, Visconte F, Raia M, Scalia G, Loffredo S, Varricchi G, Galdiero MR, Granata F, Del Vecchio L, Portella G and Marone G. (2017). Lipopolysaccharide-elicited TSLPR expression enriches a functionally discrete subset of human CD14+ CD1c+ monocytes. J Immunol, 198: 3426–3435. Link

Casas-Vila N*, Bluhm A*, Sayols S*, Dinges N, Dejung M, Altenhein T, Kappei D, Altenhein B, Roignant JY and Butter F. (2017). The developmental proteome of Drosophila melanogaster. Genome Res, 27: 1273–1285. (*indicates joint contribution) Link

Dinges N, Morin V, Kreim N, Southall TD and Roignant JY. (2017). Comprehensive characterization of the complex lola locus reveals a novel role in the octopaminergic pathway via tyramine beta-hydroxylase regulation. Cell Rep, 21: 2911–2925. Link

Dzama MM, Nigmatullina L, Sayols S, Kreim N and Soshnikova N. (2017). Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cells. Dev Biol, 432: 258–264. Link

Jahn A*, Rane G*, Paszkowski‐Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño‐Vallejo JA, Kumar AP, Buchholz F#, Butter F# and Kappei D#. (2017). ZBTB48 is both a vertebrate telomere‐binding protein and a transcriptional activator. EMBO Rep, 18: 929–946. (*indicates joint contribution, #indicates joint correspondence) Link

Kazakevych J, Sayols S, Messner B, Krienke C and Soshnikova N. (2017). Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells. Nucleic Acids Res, 45: 5770–5784. Link

Nigmatullina L, Norkin M, Dzama MM, Messner B, Sayols S and Soshnikova N. (2017). Id2 controls specification of Lgr5+ intestinal stem cell progenitors during gut development. EMBO J, 36: 869–885. Link

Sanchez-Mut JV, Heyn H, Vidal E, Delgado-Morales R, Moran S, Sayols S, Sandoval J, Ferrer I, Esteller M and Gräff J. (2017). Whole genome grey and white matter DNA methylation profiles in dorsolateral prefrontal cortex. Synapse, 71: e21959. Link

Zapata L, Susak H, Drechsel O, Friedländer MR, Estivill X and Ossowski S. (2017). Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes. Sci Rep, 7: 13124. Link

2016

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U and Garnett MJ. (2016). A landscape of pharmacogenomic interactions in cancer. Cell, 166: 740–754. Link

Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrade-Navarro MA, Poeck B, Helm M and Roignant JY. (2016). m6A modulates neuronal functions and sex determination in Drosophila. Nature, 540: 242–247. Link

Movassat M, Crabb TL, Busch A, Yao C, Reynolds DJ, Shi Y and Hertel KJ. (2016). Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns. RNA Biol, 13: 646–655. Link

Papadopoulou T, Kaymak A, Sayols S and Richly H. (2016). Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation. Cell Cycle, 15: 1479–1493. Linkhttp://dx.doi.org/10.1080/15384101.2016.1175797

Sayols S, Scherzinger D and Klein H. (2016). dupRadar: A bioconductor package for the assessment of PCR artifacts in RNA-Seq data. BMC Bioinf, 17: 428. Link

2015

Busch A and Hertel KJ. (2015). Splicing predictions reliably classify different types of alternative splicing. RNA, 21: 813–823. Link

Simon M, Richard EM, Wang X, Shahzad M, Huang VH, Qaiser TA, Potluri P, Mahl SE, Davila A, Nazli S, Hancock S, Yu M, Gargus J, Chang R, Al-Sheqaih N, Newman WG, Abdenur J, Starr A, Hegde R, Dorn T, Busch A, Park E, Wu J, Schwenzer H, Flierl A, Florentz C, Sissler M, Khan SN, Li R, Guan MX, Friedman TB, Wu DK, Procaccio V, Riazuddin S, Wallace DC, Ahmed ZM, Huang T and Riazuddin S. (2015). Mutations of human NARS2, encoding the mitochondrial asparaginyl-tRNA synthetase, cause nonsyndromic deafness and Leigh syndrome. PLoS Genet, 11: e1005097. Link

Villanueva A, Portela A, Sayols S, Battiston C, Hoshida Y, Méndez-González J, Imbeaud S, Letouzé E, Hernandez-Gea V, Cornella H, Pinyol R, Solé M, Fuster J, Zucman-Rossi J, Mazzaferro V, Esteller M and Llovet JM. (2015). DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma. Hepatology, 61: 1945–1956. Link

2014

Acebron SP, Karaulanov E, Berger BS, Huang YL and Niehrs C. (2014). Mitotic Wnt signaling promotes protein stabilization and regulates cell size. Mol Cell, 54: 663–674. Link

de Albuquerque BFM, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJT, Klein H, Boxem M and Ketting RF. (2014). PID-1 is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegans. Genes Dev, 28: 683–688. Link

Fröhlich D, Kuo WP, Frühbeis C, Sun JJ, Zehendner CM, Luhmann HJ, Pinto S, Toedling J, Trotter J and Krämer-Albers EM. (2014). Multifaceted effects of oligodendroglial exosomes on neurons: Impact on neuronal firing rate, signal transduction and gene regulation. Philos Trans R Soc Lond B Biol Sci, 369: 20130510. Link

Malone CD, Mestdagh C, Akhtar J, Kreim N, Deinhard P, Sachidanandam R, Treisman J and Roignant JY. (2014). The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript. Genes Dev, 28: 1786–1799. Link

Simonetti M, Agarwal N, Stösser S, Bali KK, Karaulanov E, Kamble R, Pospisilova B, Kurejova M, Birchmeier W, Niehrs C, Heppenstall P and Kuner R. (2014). Wnt-fzd signaling sensitizes peripheral sensory neurons via distinct noncanonical pathways. Neuron, 83: 104–121. Link

2013

Schäfer A, Karaulanov E, Stapf U, Döderlein G and Niehrs C. (2013). Ing1 functions in DNA demethylation by directing Gadd45a to H3K4me3. Genes Dev, 27: 261–273. Link

2012

Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C and Barillot E. (2012). ncPRO-seq: A tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics, 28: 3147–3149. Link


Publications acknowledging the Bioinformatics Core Facility

2018

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A and Ketting RF. (2018). Tdrd6a regulates the aggregation of buc into functional subcellular compartments that drive germ cell specification. Dev Cell, 46: 285–301.e9.

Tiwari N, Pataskar A, Péron S, Thakurela S, Sahu SK, Figueres-Oñate M, Marichal N, López-Mascaraque L, Tiwari VK and Berninger B. (2018). Stage-specific transcription factors drive astrogliogenesis by remodeling gene regulatory landscapes. Cell Stem Cell, 23: 557–571.e8.

2017

Navandar M, Garding A, Kumar Sahu S, Pataskar A, Schick S and Tiwari VK. (2017). ERK signalling modulates epigenome to drive epithelial to mesenchymal transitionOncotarget, 8: 29269–29281.

Sahu SK, Tiwari N, Pataskar A, Zhuang Y, Borisova M, Diken M, Strand S, Beli P and Tiwari VK. (2017). FBXO32 promotes microenvironment underlying epithelial-mesenchymal transition via CtBP1 during tumour metastasis and brain developmentNat Commun, 8: 1523.

Wilhelm T, Byrne J, Medina R, Kolundžić E, Geisinger J, Hajduskova M, Tursun B and Richly H. (2017). Neuronal inhibition of the autophagy cucleation complex extends life span in post-reproductive C. ElegansGenes Dev, 31: 1561–1572.

2016

Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD and Ketting RF. (2016). Enhancers reside in a unique epigenetic environment during early zebrafish developmentGenome Biol, 17: 146.

Pataskar A, Jung J, Smialowski P, Noack F, Calegari F, Straub T and Tiwari VK. (2016).  NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal programEMBO J, 35: 24–45.

Thakurela S, Garding A, Jung RB, Müller C, Goebbels S, White R, Werner HB and Tiwari VK. (2016).  The transcriptome of mouse central nervous system myelinSci Rep, 6: 25828.

2015

de Albuquerque BF, Placentino M and Ketting RF. (2015). Maternal piRNAs are essential for germline development following de novo establishment of endo-siRNAs in Caenorhabditis elegans. Dev Cell, 34: 448-56.

Sahu SK, Garding A, Tiwari N, Thakurela S, Toedling J, Gebhard S, Ortega F, Schmarowski N, Berninger B, Nitsch R, Schmidt M and Tiwari VK. (2015). JNK-dependent gene regulatory circuitry governs mesenchymal fateEMBO J, 34: 2162–2181.

Schick S, Fournier D, Thakurela S, Sahu SK, Garding A and Tiwari VK. (2015). Dynamics of chromatin accessibility and epigenetic state in response to UV damageJ Cell Sci, 128: 4380–4394.

Thakurela S, Sahu SK, Garding A and Tiwari VT. (2015). Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity. Genome Res, 25: 1309-24.

2013

de Albuquerque BFM, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJT, Klein H, Boxem M and Ketting RF. (2014). PID-1 Is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegansGenes Dev, 28: 683–688.